condo create problems with samtools

[LisaBlazek]

hallo! i have a problem with samtools after creating the condo environment:

conda create deviaTE -c r -c defaults -c conda-forge -c bioconda -c w-l -n deviaTE_env
#and
#like you suggested in another ticket
conda create deviaTE==0.3.7 -c r -c defaults -c conda-forge -c bioconda -c w-l -n deviaTE_env 

if i want to run samtools in the deviaTEenv i get an error: **samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory_**

i found out that this is an known conda bug and tried to update samtools

conda install -c bioconda samtools=1.9 --force-reinstall
#or 
conda config --add channels bioconda
conda config --add channels conda-forge
conda install samtools==1.11

but nothing helped. maybe you have some insight? i was really looking forward on using this program! kind regards, lisa

[W-L]

Hi Lisa, Thanks for getting in touch! This is something I have seen a few times before, especially on MacOS. As far as I understand, this is because samtools has some trouble with missing links to the mentioned libcrypto library.

Here's what helped to solve this in the past:

• Make sure that openssl is installed system-wide
• then link the missing libraries manually

brew install openssl
[or]
conda install openssl

ln -s /usr/local/opt/openssl/lib/libcrypto.1.0.0.dylib /usr/local/lib/
ln -s /usr/local/opt/openssl/lib/libssl.1.0.0.dylib /usr/local/lib/

I hope this helps, please keep me updated! Lukas

[LisaBlazek]

hello! i tried to install openssl and this kinda worked, openssl was in my path but i could not locate the two missing libraries. as an alternative i tried to install the program with pip and used it on you test data and this worked, i got the same pdf. so i think i'm gonna close the ticket. thank you for your fast reply and help!!!